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dc.contributor.authorMuhammod, Rafsanjani
dc.contributor.authorAhmed, Sajid
dc.contributor.authorFarid, Dewan Md
dc.contributor.authorShatabda, Swakkhar
dc.contributor.authorSharma, Alok
dc.contributor.authorDehzangi, Abdollah
dc.date.accessioned2019-07-12T04:24:26Z
dc.date.available2019-07-12T04:24:26Z
dc.date.issued2019
dc.identifier.issn1367-4803
dc.identifier.doi10.1093/bioinformatics/btz165
dc.identifier.urihttp://hdl.handle.net/10072/386354
dc.description.abstractMOTIVATION: Extracting useful feature set which contains significant discriminatory information is a critical step in effectively presenting sequence data to predict structural, functional, interaction and expression of proteins, DNAs, and RNAs. Also, being able to filter features with significant information and avoid sparsity in the extracted features require the employment of efficient feature selection techniques. Here we present PyFeat as a practical and easy to use toolkit implemented in Python for extracting various features from proteins, DNAs, and RNAs. To build PyFeat we mainly focused on extracting features that capture information about the interaction of neighboring residues to be able to provide more local information. We then employ AdaBoost technique to select features with maximum discriminatory information. In this way, we can significantly reduce the number of extracted features and enable PyFeat to represent the combination of effective features from large neighboring residues. As a result, PyFeat is able to extract features from 13 different techniques and represent context free combination of effective features. The source code for PyFeat standalone toolkit and employed benchmarks with a comprehensive user manual explaining its system and workflow in a step by step manner are publicly available. RESULTS: https://github.com/mrzResearchArena/PyFeat/blob/master/RESULTS.md. AVAILABILITY: Toolkit, source code, and manual to use PyFeat: https://github.com/mrzResearchArena/PyFeat/.
dc.description.peerreviewedYes
dc.languageEnglish
dc.language.isoeng
dc.publisherOxford Academic
dc.relation.ispartoflocationEngland
dc.relation.ispartofjournalBioinformatics
dc.subject.fieldofresearchMathematical sciences
dc.subject.fieldofresearchBiological sciences
dc.subject.fieldofresearchcode49
dc.subject.fieldofresearchcode31
dc.titlePyFeat: A Python-based Effective Feature Generation Tool for DNA, RNA, and Protein Sequences.
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
dc.description.versionAccepted Manuscript (AM)
gro.description.notepublicThis publication has been entered into Griffith Research Online as an Advanced Online Version.
gro.rights.copyright© 2019 Oxford University Press. This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Bioinformatics following peer review. The definitive publisher-authenticated version PyFeat: a Python-based effective feature generation tool for DNA, RNA and protein sequences, Bioinformatics, is available online at: https://doi.org/10.1093/bioinformatics/btz165.
gro.hasfulltextFull Text
gro.griffith.authorSharma, Alok


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